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/*
* Copyright (C) 2014-2021 Brian L. Browning
*
* This file is part of Beagle
*
* Beagle is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Beagle is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package vcf;
import ints.IntArray;
/**
* <p>Interface {@code DuplicatesGTRec} represents marker alleles for a
* list of samples. The samples in the list of samples are not
* required to be unique.
* </p>
* All instances of {@code HapsMarkers} are required to be
* immutable.
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public interface DuplicatesGTRec extends MarkerContainer, IntArray {
/**
* Returns the first allele for the specified sample or
* -1 if the allele is missing. The two alleles for a sample
* are arbitrarily ordered if
* {@code this.unphased(marker, sample) == false}.
* @param sample a sample index
* @return the first allele for the specified sample
*
* @throws IndexOutOfBoundsException if
* {@code sample < 0 || sample >= this.size()/2}
*/
int allele1(int sample);
/**
* Returns the second allele for the specified sample or
* -1 if the allele is missing. The two alleles for a sample
* are arbitrarily ordered if
* {@code this.unphased(marker, sample) == false}.
* @param sample a sample index
* @return the second allele for the specified sample
*
* @throws IndexOutOfBoundsException if
* {@code sample < 0 || sample >= this.size()/2}
*/
int allele2(int sample);
/**
* Returns the specified allele for the specified haplotype or
* -1 if the allele is missing. The two alleles for a sample
* at a marker are arbitrarily ordered if
* {@code this.unphased(marker, hap/2) == false}.
* @param hap a haplotype index
* @return the specified allele for the specified sample
*
* @throws IndexOutOfBoundsException if
* {@code hap < 0 || hap >= this.size()}
*/
@Override
int get(int hap);
/**
* Returns an array of length {@code this.size()} whose {@code j}-th
* element is equal to {@code this.allele(j}}
* @return an array of length {@code this.size()} whose {@code j}-th
* element is equal to {@code this.allele(j}}
*/
int[] alleles();
/**
* Returns the number of haplotypes.
* @return the number of haplotypes
*/
@Override
int size();
/**
* Returns {@code true} if the genotype for the specified sample
* has non-missing alleles and is either haploid or diploid with
* a phased allele separator, and returns {@code false} otherwise.
* @param sample a sample index
* @return {@code true} if the genotype for the specified sample
* is a phased, nonmissing genotype
*
* @throws IndexOutOfBoundsException if
* {@code sample < 0 || sample >= this.size()/2}
*/
boolean isPhased(int sample);
/**
* Returns {@code true} if every genotype for each sample is a phased,
* non-missing genotype, and returns {@code false} otherwise.
* @return {@code true} if the genotype for each sample is a phased,
* non-missing genotype
*/
boolean isPhased();
}
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